NM_022124.6(CDH23):c.3009T>C (p.Ser1003=) AND not specified

Clinical significance:Benign (Last evaluated: May 7, 2014)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000037087.4

Allele description [Variation Report for NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)]

NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)

Gene:
CDH23:cadherin related 23 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)
Other names:
p.S1003S:TCT>TCC
HGVS:
  • NC_000010.11:g.71706952T>C
  • NG_008835.1:g.315006T>C
  • NM_001171930.2:c.3009T>C
  • NM_001171931.2:c.3009T>C
  • NM_022124.6:c.3009T>CMANE SELECT
  • NP_001165401.1:p.Ser1003=
  • NP_001165402.1:p.Ser1003=
  • NP_071407.4:p.Ser1003=
  • NC_000010.10:g.73466709T>C
  • NM_001171931.1:c.3009T>C
  • NM_022124.5:c.3009T>C
  • c.3009T>C
  • p.Ser1003Ser
Links:
dbSNP: rs10823829
NCBI 1000 Genomes Browser:
rs10823829
Molecular consequence:
  • NM_001171930.2:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171931.2:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022124.6:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
378

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000060744Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Dec 28, 2012)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV000167605GeneDxcriteria provided, single submitter
Benign
(Mar 5, 2013)
germlineclinical testing

Citation Link,

SCV000228381EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(May 7, 2014)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided379378not providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

CDH23 mutation and phenotype heterogeneity: a profile of 107 diverse families with Usher syndrome and nonsyndromic deafness.

Astuto LM, Bork JM, Weston MD, Askew JW, Fields RR, Orten DJ, Ohliger SJ, Riazuddin S, Morell RJ, Khan S, Riazuddin S, Kremer H, van Hauwe P, Moller CG, Cremers CW, Ayuso C, Heckenlively JR, Rohrschneider K, Spandau U, Greenberg J, Ramesar R, Reardon W, et al.

Am J Hum Genet. 2002 Aug;71(2):262-75. Epub 2002 Jun 19.

PubMed [citation]
PMID:
12075507
PMCID:
PMC379159

Survey of the frequency of USH1 gene mutations in a cohort of Usher patients shows the importance of cadherin 23 and protocadherin 15 genes and establishes a detection rate of above 90%.

Roux AF, Faugère V, Le Guédard S, Pallares-Ruiz N, Vielle A, Chambert S, Marlin S, Hamel C, Gilbert B, Malcolm S, Claustres M; French Usher Syndrome Collaboration..

J Med Genet. 2006 Sep;43(9):763-8. Epub 2006 May 5.

PubMed [citation]
PMID:
16679490
PMCID:
PMC2564578
See all PubMed Citations (7)

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000060744.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided379not providednot providedclinical testing PubMed (7)

Description

Ser1003Ser in Exon 26A of CDH23: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 33.2% (1436/4326) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs10823829).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided379not provided378not provided

From GeneDx, SCV000167605.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000228381.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 16, 2021

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